Lost and Found
by ThreeWishes123
Summary: Molly has been kidnapped and Sherlock has 48 hours to find her.
1. The Dark Room

**This is my first Sherlock/Molly fanfic. I hope you enjoy :)**

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**Chapter 1 – The Dark Room**

'_Is that a plane?'_ was the first thought that popped into Molly's head as she slowly woke up. She hadn't opened her eyes yet and was just listening to the sounds around her. She realised with a start that she wasn't hearing the normal early morning noises in her flat. As she woke up more, she tried to open her eyes but found that there was something preventing her from doing so. Her heart started to race as panic set in. A dull throbbing in the back of her head told her the reason that she had been unconscious and not asleep as she had thought. Molly tried to move and felt rope around her wrists and ankles, tying her to a chair. Taking a few deep breaths, '_it will do you no good to panic now,'_ she relaxed slightly and tried to determine where she was. There was a slight echo in the room but it didn't seem too large, she listened harder but only heard the traffic from outside, which gave nothing away. Sniffing the air also gave her no clues, just the smell of mildew and rot. Other than those two facts, she had nothing. She couldn't even get her shoes off to see whether she was on carpet or cement. As she was considering how she had gotten here, she heard faint voices coming from behind her. Panic started to bubble again when she heard the door behind her open and the voices stopped. Footsteps got closer and Molly could feel a warm breath in her ear. "Hello darling, did you miss me?"

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Sherlock waltzed into the lab like he normally did, making a grand entrance only to find that there was no one to see his spectacular entrance. Slightly disappointed but mostly unfazed, he moved to where the microscopes were and commenced looking at some tissue samples he had gathered at a crime scene. It only took him minutes to find out how the victim had died and as he was firing off a text to Lestrade he heard the lab doors open and shut as someone entered. "Ah Molly, finally. I need your help with… You're not Molly." When Sherlock had raised his head, he had realised that another lab assistant had walked in and not Molly. The lab assistant looked confused, "no I'm not. Molly hasn't come in today. I thought that you knew that?" Sherlock looked at the assistant, deducing him, 'j_ust finished university. For the second time. Lives alone with two goldfish. Hasn't spoken to his parents in 2 years... conclusion: not important.'_ Sherlock returned to his phone as he finished the message and got up to leave. As he reached the door, the other man grabbed his arm, "sweet girl, that Molly. I wonder where she has gone?" Sherlock stopped immediately and looked at him, the assistant giving him a wink and moved over to the chemical storage. Watching the other man for a few more seconds, Sherlock fled the lab and out to the street to hail a cab. He gave Molly's address to the cabby and they headed towards her flat. On the way Sherlock tried three times to get in contact with her but failed. He started to worry.

Sherlock and Molly had become quite close during the years while he was 'dead'. She had helped him during and immediately after the fall, housing him in her flat as he recovered from the few injuries he had suffered jumping off of Bart's. Over the two years he was hunting down Moriarty's Network, he had occasionally taken refuge in her flat. She had taken all the bad thoughts of what he was doing and soothed him as he mourned the loss of his friends. During those times, he had craved human contact like he had never needed to before and Molly was always there to give it. It was always at night he was worst, having nightmares about the work he was doing, and that's where Molly came to him, soothing him back to sleep, knowing exactly what he needed in his moments of weakness. It wasn't until one night after months of no contact, that he had acted on the urges he never knew he had. Afterwards Sherlock had fallen into a dreamless sleep, feeling at peace for a few hours. The next morning Sherlock had to leave but not without a passionate kiss from Molly as he left and after that he knew that what he was doing was truly worth it.

Sherlock threw some money at the driver as he dove out of the cab and up the stairs to Molly's door. He used his spare key to get in, knowing if Molly was home, she wouldn't mind. When he stepped inside, he felt that the flat was empty and very quiet. Slowly moving through to the living room and into the kitchen, he saw that nothing seemed out of place. There was no sign of a struggle nor was there sign that Molly had just decided to go on a holiday. A bad feeling settled in Sherlock's stomach as he moved down the hall into her bedroom. Once again nothing was amiss until he turned to look at the bed. Written in large red letters above her bed were the words 'DID YOU MISS ME?'


	2. Clues

**Chapter 2 – Clues**

The voice in here ear sent shivers up her spine. She would recognise that voice anywhere. "Hello Jim." Molly surprised herself with how calm her voice sounded. "Ah Molly dear. Such a pleasure to see you again. I missed you my pet." She cringed at the petname he had given her while they had been dating. Molly blinked as the blindfold was removed from her eyes. She took in her surroundings. They seemed to be in some kind of basement, which explained the smell. The room was empty except for a mattress lying on the ground opposite here. The only source of light was from a single light bulb hanging from the ceiling. The walls were bare and it seemed the only exit was the door that she knew was behind her. "What do you want with me Jim?" Molly spat at him, glaring at him as he moved to kneel in front of her. "Oh darlin', it's not you I want. It's Sherlock. See it wasn't very fair of him to fake his death, he cheated in this little game of ours and now he needs to pay." Molly's heart quickened at the menacing glare that Moriarty gave her but she tried hard to not let it show. "So why do you need me?" He chuckled, "well my dear, it seems that Sherlock had a helping hand and my guess is that it was little old you." The devilish grin he gave her sent chills down her spine.

* * *

"But he died, Sherlock! You saw it with your own damn eyes!" John had been the first person to arrive at Molly's flat after Sherlock had made his discovery. Soon after him Lestrade had followed with a forensic team. "I know he is supposed to be dead, John, but so am I." John glared at him, "and if I can fake my death with only Molly and a few of my homeless network then obviously Moriarty can do it with a criminal network behind him." Sherlock looked back at the words painted on the wall, it had only taken him seconds to work out that they weren't written in blood but just red paint. Sherlock had made sure to look all through the apartment to make sure that there weren't any clues that he had missed. He was disappointed but not surprised that he found none. As the forensic team did their job, Sherlock and John walked outside to get out of their way. Sherlock leaned against the wall of the hallway and steepled his fingers, going into his mind place to sort out what little information he knew. John, knowing he wasn't going to get anything out of Sherlock, went back into the flat to see what the team had found. Sherlock didn't need long in his head and as he was coming back to the real world, his phone rang. He noted the message 'blocked number' and knew that it could only be one person. "Hello Sherlock." "Hello Jim." Sherlock replied. "I'd love to know how you pulled it off, Sherlock. But let's save that conversation for another day, I believe we have more pressing matters to attend to. Are you missing her yet?" Sherlock considered very carefully about what he wanted to say, knowing that Jim would take advantage of knowing Molly was more important to him than just the woman who helped him disappear. "What do you want with her? I assume you found out that she was an important part of my survival." He hoped that Jim wouldn't hear the desperation that had crept into his voice, he needed to hear Molly. "You cheated my dear, and you need to pay. She helped you so she also needs to be punished." Sherlock heard the faint gasp in the background and knew it was Molly. '_She is still alive'_ he breathed a mental sigh of relief. "Okay Sherlock, this is how our new game is going to go. Every hour I'm going to send you a clue to her location, they will get more specific as time goes on. However you only have 48 hours to find here and if you haven't found her within the first 24, well let's just say, you will get some incentive to work harder."


	3. The Game

**Chapter 3 – The Game**

Molly was beginning to feel hungry. She didn't know how long it had been since she last ate. One of Jim's henchmen had been bringing her glasses of water every so often but she hadn't seen any food. She had no idea what time of day it was, there was nothing in the room to give her any indication. Due to her unusual hours at the hospital, her body clock was no use. Molly knew about the challenge that had been set for Sherlock, however doubt played in her mind as she wondered how much effort Sherlock would put into finding her. She knew that the dynamics of their relationship had changed in the two years he had gone but now that he had been back for months now and she had only seen him intimately a few times, when the memories and dreams had gotten too bad for him to handle. Molly heard the door behind here open for what seemed like the hundredth time and a wonderful smell hit her. Jim moved in front of her, holding a plate with a chicken burger on it. "Hungry pet?" Molly nodded slightly, trying not to give away just how hungry she was. "Now do you promise to behave if I untie one of your hands?" She nodded again. Jim reached for her right wrist and loosened the rope until her hand came free. Molly flexed her wrist and fingers, grateful for the small amount of movement. She reached out for the burger in her lap and took a bite. Jim watched her as she ate slowly, wanting to savour it, as she didn't know when the next time she would get the chance. "So it's been 12 hours now Molls, I wonder what Sherlock is up to? Hmm, just think, 12 more hours and we get to have some fun." The grin on his face made her want to bring the chicken burger back up. Jim retied her arm to the chair and left the room, laughing the whole time.

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Sherlock was getting more and more frustrated as time went on. Once Moriarty had hung up he had sent the first text _Earth_, it had almost made Sherlock hurl his phone at the wall. The next six texts weren't any better. The second one had just said _land,_ others had said _Europe, UK, England _and _London._ The forensic team hadn't picked up anything in the flat, as Sherlock knew they wouldn't. '_Waste of time,"_ he thought as he travelled back to Baker Street with John. Over the next six hours, Sherlock had become increasingly frustrated and worried. The only clues Moriarty had sent him gave vague details of apartment buildings (_room, no windows, basement)_ and Sherlock knew that he wasn't going to get any more specific than that. He began to doubt that he could find her before the 24 hours were up. '_I need her home safe and unhurt.' _He didn't know where these new feelings were coming from and they weren't overly welcome, but only because he was on a case and right now the last thing he wanted was to be distracted.

Over the next twelve hours, the messages from Moriarty came and Sherlock slowly got closer to where Molly was. Moriarty seemed to be guiding him to the south side of the Thames. Sherlock watched as the clock showed that his 24 hours were up, and he dropped to his knees in defeat. His phone rang beside him, reluctantly he answered it. Immediately he wanted to hang up, all he could hear on the other end was Molly's moans and shouts of pain. Jim's cold voice spoke to him, "one mark for each hour you lose, Sherlock."


	4. You Lose Some, You Win Some

**Chapter 4 – You lose some, you win some**

Molly could feel the blood running down her back. She knew the cuts weren't long but were deep enough to scar. "Just keeping tally for the hours, my dear pet," Jim had told her, "a little reminder for Sherlock." There were now four lines on her shoulder and she knew a fifth was coming soon. Molly quietly sobbed, she had started losing faith that Sherlock was ever going to find her. The door clicked open behind her and she held her breath in anticipation.

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Sherlock was frantic. Moriarty had slipped up when he had called him. Once the moans of Molly in the background had died out he could hear the rumbling of an airplane, which meant that the building that Molly was being kept at had to be directly under a flight path. Sherlock had located a number of possible buildings that it could have been. He had started to ignore the texts from the madman as they were still no help in distinguishing which building it was. That was until his 30th text. _6 floors up._ There were only two buildings that it could have been. He knew that he only had an hour before Molly was going to get hurt again so he had to act fast. Employing a few of his homeless network to investigate the two buildings. While all this was happening he had informed Mycroft and Lestrade of his discovery but told them to wait until he was sure. He wanted Moriarty too and wanted him dead. When the correct building was discovered, Sherlock and John had taken a cab as quickly as they could to the street it was on.

They entered the building as quietly as they could. Sherlock could hear muffled voices coming from down stairs. He and John both withdrew their guns. At the bottom of the stairs, they came across their first obstacle. Two men stood at a door, Sherlock recognised one as the man he had met at the lab two days ago. Easily they took the men out and moved on. Behind the next door, they could hear tiny whimpers as well as the occasional cold giggle. Sherlock's heart sped up but as he rushed to the door, John held him back. "Be reasonable Sherlock. We need to send your brother a message and then we can go ahead," Sherlock heard the reason in his voice and sent the message to Mycroft. Slowly Sherlock opened the basement door. Both Molly and Moriarty had their backs to Sherlock and John, which made what happened next easier. Sherlock moved up behind Moriarty while John kept his gun trained on him. Jim let out a shout of surprise as Sherlock quickly handcuffed him and knocked him out. Throwing the madman to the side he immediately went to Molly. She looked so pale but her eyes lit up when she saw Sherlock. He quickly undid the ropes binding her and pulled her into his arms.

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Moriarty had just come into the room and was about to make his 6th mark when she heard the slight click of the door. She held her breath when she felt movement behind her. A thud and a click later, she looked up to see Sherlock's ice blue eyes staring back at her. Relief filled her as he pulled her into his arms. Her only thoughts were how good it felt to be in his arms. Distantly she could hear more people enter the room but refused to leave Sherlock's arms, even when the paramedics came down. Sherlock had to carry her up to the ambulance and hold her as they treated the cuts on her back. Once they had finished, Molly looked out to the scene outside the ambulance. Just as she looked up, two policemen were bringing the handcuffed but conscious Moriarty out of the building. He locked eyes with her and grinned sadistically and she knew this wasn't going to be over until he was dead.

Sherlock felt Molly slightly twist in his arms, unaware of what she was doing until it was too late. The gun let off a loud bang and Moriarty slipped out of the officer's hands and landed on the ground, dead. Everyone turned to look at them in the ambulance, Molly dropped the gun and curled into his chest. A few raced forward towards them but all Sherlock was focusing on was Molly's small voice repeating, "It's over."

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A/N: So I decided to post the whole story because I was pretty happy with it. Was thinking of writing an epilogue but would love some reviews if you want one! thanks for reading :)


	5. Epilogue

**Epilogue**

Molly had only had to stay in the hospital overnight for observation. The cuts on her back were not deep but would leave a faint scar that would fade over time. The day she was released, Sherlock had insisted that she stay at Baker Street with him. Molly wanted to protest, knowing that she would be safe in her own flat now that Moriarty was dead, but Sherlock wouldn't listen.

The nightmares didn't start until the third night after her release. Sherlock had taken on a small case from Lestrade so Molly was sleeping in his bed. It was midnight when Sherlock heard a loud thud come from his bedroom. He thought nothing of it until he heard her scream. Racing to the bedroom, he pulled open the door, "Molly?!" Sherlock's eyes darted around the bedroom and finally settled on Molly's small form, writhing on the floor. She had fallen off the bed and had gotten tangled in the blankets in her fits. "Sherlock help! He's got me!" Molly's screams had him rushing to her side in a flash and he struggled to hold her down as he tried to rouse her. Freeing her from the blankets, Sherlock cradled her in his arms while her breathing returned to normal. "It's okay Molly, I've got you. You're safe, he can't hurt you anymore," Sherlock soothed. He lifted her off the floor and placed her on the bed, joining her when she wouldn't let go of his shirt. Molly curled herself into a ball against his chest and Sherlock hugged her close. Sherlock wanted to reciprocate the same comfort that she had for him when he had his nightmares. He noticed that Molly had stopped shaking and he peered down at her. She was looking up at him with her big doe eyes, slightly red rimmed from crying. He gently swept a few loose strands of hair behind her ear and rested his hand on her cheek gently. Molly wriggled up until her face was level with his. He stared into her eyes for a moment, when he felt two delicate hand slide under his shirt. He leaned his forehead against Molly's and gently rolled Molly underneath him. As she undid the buttons on his shirt, he ghosted kisses over her nose, forehead and cheeks. He covered her lips with his as she removed his shirt. The kiss started out slow, unlike the other times they had been together, but soon become passionate.

Molly awoke the next morning to the feeling of light touches on her back. She turned her head to see Sherlock running his fingers down the faint scars on her back. There was a look of sadness in his eyes and he couldn't look directly at her. "Molly, I'm so sorry," Sherlock sighed. Molly completely turned over to face him and took his face into her hands, "Sherlock, look at me," his eyes darted to hers, "it was not your fault. Moriarty is a madman and is the only one to blame," she said with determination. Her thumbs caressed Sherlock's cheeks and pulled his face down so she could gently kiss him. Sherlock broke the kiss and pulled her into a tight embrace. Molly wrapped her arms around his shoulders and ran her fingers through the hair at the back of his head, trying to soothe him. They stayed like that for a few minutes until Molly moved to look at him again. The sadness in his eyes was replaced with something else that Molly couldn't quite place. "Molly there is something I want to say, I don't really know how to say it so I'm just going to give it a go," Sherlock took a deep breath and Molly's heartbeat quickened, "I am very grateful to have you as a friend, I don't believe I could have gotten through the past two years without your help. I've never been the sentimental type, I always considered it a weakness but watching you over the years I have come to see it as a strength. Whenever I was away fighting Moriarty's network, I would think of the people who I had left behind, John, Lestrade, Mrs Hudson and especially you and I would feel stronger. Since I have been back, I've been trying to fight the feelings I have had out of old habits but those 30 hours that I thought I was going to lose you made me see that I wanted to stop fighting and just give in. I'm not perfect and I will slip, probably more than once but I know, well I hope, that you can put up with me. So that being said, I was hoping that maybe you would like to move here with me?" Molly stared at Sherlock, frozen in shock. His words running though her head over and over. '_Oh gosh,'_ was her only thought. After a few more seconds, Molly came back to herself, "of course I will you great git! I've put up with you though all your moments, and I always come back. I love you Sherlock Holmes."

Sherlock felt his heartbeat quicken at her last words. 'So_ this is what all the fuss is about,'_ he thought. He reached over to Molly and brushed a few stray tears off her cheek and pulled her into a kiss, conveying all the things he couldn't say. The pair stayed in bed for a few more hour until both bellies were calling out for food and Molly pulled Sherlock into the kitchen for breakfast and to start their new life together.

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A/N: Thank you everyone for reading and reviewing! it means a lot :) :) I hope you are satisfied with the epilogue and I hope Sherlock isn't too much out of character. I was toying with the idea of writing smut but it turned out terrible and i started giggling like a 10 year old boy who had heard the word 'boobies' for the first time... sad. anyway, I have another fluffy story on the way, so stay tuned! thanks all xx


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